I think it would be fine. Charlotte is a lovely name and your DH may soften to it so much that he can't bear to shorten it!

Even if you do go with the Charlie nickname, I don't think it would be a major deal. I know a family with 5 girls called Olivia, all named after their grandmother and they love it. Also, in my family, my cousin's name is Sarah-Rose, her aunt was Sarah and two other cousins were named Sarah and Rose. They all love the connection their names gave them. They all had different surnames and their first names tied them all together.

Otherwise, as suggested Lottie is also a lovely nickname, as is Charlie but pronounced as the name Charlotte is pronounced - Sharlie.